4U2C

Crystal structure of dienelactone hydrolase A-6 variant (S7T, A24V, Q35H, F38L, Q110L, C123S, Y145C, E199G and S208G) at 1.95 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search.

Porter, J.L.Boon, P.L.Murray, T.P.Huber, T.Collyer, C.A.Ollis, D.L.

(2015) ACS Chem Biol 10: 611-621

  • DOI: 10.1021/cb500809f
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The ease with which enzymes can be adapted from their native roles and engineered to function specifically for industrial or commercial applications is crucial to enabling enzyme technology to advance beyond its current state. Directed evolution is a ...

    The ease with which enzymes can be adapted from their native roles and engineered to function specifically for industrial or commercial applications is crucial to enabling enzyme technology to advance beyond its current state. Directed evolution is a powerful tool for engineering enzymes with improved physical and catalytic properties and can be used to evolve enzymes where lack of structural information may thwart the use of rational design. In this study, we take the versatile and diverse α/β hydrolase fold framework, in the form of dienelactone hydrolase, and evolve it over three unique sequential evolutions with a total of 14 rounds of screening to generate a series of enzyme variants. The native enzyme has a low level of promiscuous activity toward p-nitrophenyl acetate but almost undetectable activity toward larger p-nitrophenyl esters. Using p-nitrophenyl acetate as an evolutionary intermediate, we have generated variants with altered specificity and catalytic activity up to 3 orders of magnitude higher than the native enzyme toward the larger nonphysiological p-nitrophenyl ester substrates. Several variants also possess increased stability resulting from the multidimensional approach to screening. Crystal structure analysis and substrate docking show how the enzyme active site changes over the course of the evolutions as either a direct or an indirect result of mutations.


    Organizational Affiliation

    Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxymethylenebutenolidase
A
236Pseudomonas knackmussiiMutation(s): 9 
Gene Names: clcD
EC: 3.1.1.45
Find proteins for P0A115 (Pseudomonas knackmussii (strain DSM 6978 / LMG 23759 / B13))
Go to UniProtKB:  P0A115
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.594α = 90
b = 70.445β = 90
c = 74.089γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP120104262

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Derived calculations
  • Version 1.2: 2015-03-04
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence